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Separable roles for RNAi in regulation of transposable elements and viability in the fission yeast Schizosaccharomyces japonicus [smallRNA-Seq]

ABSTRACT: Separable roles for RNAi in regulation of transposable elements and viability in the fission yeast Schizosaccharomyces japonicus [smallRNA-Seq]

PROVIDER: PRJNA770349 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16291982.fastq.gz	Fastqsanger.gz
	SRR16291983.fastq.gz	Fastqsanger.gz
	SRR16291984.fastq.gz	Fastqsanger.gz
	SRR16291985.fastq.gz	Fastqsanger.gz

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Separable roles for RNAi in regulation of transposable elements and viability in the fission yeast Schizosaccharomyces japonicus

Project description:Separable roles for RNAi in regulation of transposable elements and viability in the fission yeast Schizosaccharomyces japonicus

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Separable roles for RNAi in regulation of transposable elements and viability in the fission yeast Schizosaccharomyces japonicus [RNA-Seq]

Project description:Separable roles for RNAi in regulation of transposable elements and viability in the fission yeast Schizosaccharomyces japonicus [RNA-Seq]

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Separable roles for RNAi in regulation of transposable elements and viability in the fission yeast Schizosaccharomyces japonicus [ChIP-Seq]

Project description:Separable roles for RNAi in regulation of transposable elements and viability in the fission yeast Schizosaccharomyces japonicus [ChIP-Seq]

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Separable roles for RNAi in regulation of transposable elements and viability in the fission yeast Schizosaccharomyces japonicus [smallRNA-Seq]

Project description:small RNA-seq was performed to identify differences in small RNA complement between wild type and Dcr1 deficent cells in Schizosaccharomyces japonicus.

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Separable roles for RNAi in regulation of transposable elements and viability in the fission yeast Schizosaccharomyces japonicus [RNA-Seq]

Project description:RNA-seq was performed to identify transcripts differentially expressed in Schizosaccharomyces japonicus cells lacking Dcr1.

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Project description:ChIP-seq was performed to identify differences in H3K9me2 profiles between wild type and Dcr1 deficent cells in Schizosaccharomyces japonicus.

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Separable roles for RNAi in regulation of transposable elements and viability in the fission yeast Schizosaccharomyces japonicus.

Project description:RNA interference (RNAi) is a conserved mechanism of small RNA-mediated genome regulation commonly involved in suppression of transposable elements (TEs) through both post-transcriptional silencing, and transcriptional repression via heterochromatin assembly. The fission yeast Schizosaccharomyces pombe has been extensively utilised as a model for studying RNAi pathways. However, this species is somewhat atypical in that TEs are not major targets of RNAi, and instead small RNAs correspond primarily to non-coding pericentromeric repeat sequences, reflecting a specialised role for the pathway in promoting heterochromatin assembly in these regions. In contrast, in the related fission yeast Schizosaccharomyces japonicus, sequenced small RNAs correspond primarily to TEs. This suggests there may be fundamental differences in the operation of RNAi pathways in these two related species. To investigate these differences, we probed RNAi function in S. japonicus. Unexpectedly, and in contrast to S. pombe, we found that RNAi is essential in this species. Moreover, viability of RNAi mutants can be rescued by mutations implicated in enhancing RNAi-independent heterochromatin propagation. These rescued strains retain heterochromatic marks on TE sequences, but exhibit derepression of TEs at the post-transcriptional level. Our findings indicate that S. japonicus retains the ancestral role of RNAi in facilitating suppression of TEs via both post-transcriptional silencing and heterochromatin assembly, with specifically the heterochromatin pathway being essential for viability, likely due to a function in genome maintenance. The specialised role of RNAi in heterochromatin assembly in S. pombe appears to be a derived state that emerged after the divergence of S. japonicus.

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Project description:To identify the genes required to sustain aneuploid viability, we screened a deletion library of non-essential genes in the fission yeast Schizosaccharomyces pombe, in which most types of aneuploidy are eventually lethal to the cell. Aneuploids remain viable for a period time and can form colonies by reducing the extent of the aneuploidy. We hypothesized that a reduction in colony formation efficiency could be used to screen for gene deletions that compromise aneuploid viability. Deletion mutants were used to measure the effects on the viability of spores derived from triploid meiosis and from a chromosome instability mutant. We found that the CCR4-NOT complex, an evolutionarily conserved general regulator of mRNA turnover, and other related factors, including poly(A)-specific nuclease for mRNA decay, are involved in aneuploid viability. Defective mutations in CCR4-NOT complex components in the distantly related yeast Saccharomyces cerevisiae also affected the viability of spores produced from triploid cells, suggesting that this complex has a conserved role in aneuploids. In addition, our findings suggest that the genes required for homologous recombination repair are important for aneuploid viability. Gene expression profile at exponentially-growing phase.in the fission yeast deletion mutants of the CCR4-NOT complex protein genes.

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